Pre-visualization of the normalized count data before any differential analysis

Load

Libraries and functions

Allowing multi-threading with up to 4 threads.
[1] "preparing gene to GO mapping data..."
[1] "preparing IC data..."
[1] "preparing gene to GO mapping data..."
[1] "preparing IC data..."
[1] "preparing gene to GO mapping data..."
[1] "preparing IC data..."

Data

	GF_104w_F_1_2	GF_104w_F_2_2	GF_104w_F_3_2	GF_104w_M_1_2	GF_104w_M_2_2	GF_52w_M_1_2	GF_52w_M_2_2	GF_52w_M_3_2	GF_52w_M_4_2	GF_8w_M_1_2	⋯	SPF_8w_F_4_2	SPF_8w_F_5_2	GF_8w_F_1_2	GF_8w_F_2_2	GF_8w_F_3_2	GF_8w_F_4_2	GF_8w_F_5_2	GF_104w_M_3_2	GF_104w_M_5_2	GF_104w_M_4_2
0610005C13Rik	0.00000	0.00000	0.00000	1.747854	1.244311	0.8338695	4.892544	5.547012	7.158344	8.384882	⋯	2.57208	0.00000	18.04370	0.00000	2.001891	5.212621	0.00000	1.243886	1.039189	1.495931
0610007P14Rik	857.59757	740.81613	899.06639	875.674692	981.138840	503.6571924	525.459208	509.215656	730.866890	597.722277	⋯	897.65596	947.91171	888.38701	674.46562	605.571925	586.941079	799.60448	490.090915	592.337898	741.981645
0610009B22Rik	1008.62104	1155.42062	1166.35639	1210.388671	1539.834260	1028.9949924	867.937277	1006.227887	869.022923	939.106744	⋯	1280.89590	1431.97437	1028.49105	1009.00917	1129.066334	949.739473	1080.92333	685.380950	802.254135	780.875844
0610009L18Rik	27.86743	35.77805	17.99933	20.100317	37.951471	31.6870419	26.419737	22.188046	4.295006	61.089852	⋯	101.59716	71.27956	47.76274	19.36265	11.010399	44.828537	24.07684	24.877711	22.862164	38.894199
0610009O20Rik	214.84887	275.70146	262.79017	223.725271	268.771071	296.8575505	346.392104	391.619012	306.377109	356.956390	⋯	225.05701	182.98632	229.26116	157.05260	268.253349	301.289471	266.11243	334.605219	364.755442	393.429783
0610010B08Rik	0.00000	0.00000	0.00000	0.000000	0.000000	0.0000000	0.000000	0.000000	0.000000	0.000000	⋯	0.00000	0.00000	0.00000	0.00000	0.000000	0.000000	0.00000	0.000000	0.000000	0.000000

Sample clustering

With all genes

Without X/Y genes

PCA

Gene co-expression network analysis

Build network

1. 24421
2. 63

1. 11170
2. 63

pickSoftThreshold: will use block size 4005.
 pickSoftThreshold: calculating connectivity for given powers...
   ..working on genes 1 through 4005 of 11170
   ..working on genes 4006 through 8010 of 11170
   ..working on genes 8011 through 11170 of 11170
   Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
1      1   0.0868  0.882          0.888 1080.000  1.09e+03 1690.00
2      2   0.2860 -1.170          0.863  336.000  3.22e+02  799.00
3      3   0.5750 -1.720          0.923  133.000  1.16e+02  460.00
4      4   0.6710 -2.020          0.935   61.500  4.70e+01  296.00
5      5   0.7370 -2.100          0.954   31.700  2.09e+01  205.00
6      6   0.7430 -2.220          0.956   17.700  9.85e+00  148.00
7      7   0.7790 -2.190          0.968   10.600  4.92e+00  111.00
8      8   0.7990 -2.150          0.974    6.640  2.53e+00   85.60
9      9   0.8190 -2.120          0.978    4.350  1.35e+00   67.20
10    10   0.8340 -2.050          0.982    2.950  7.41e-01   53.70
11    12   0.8560 -1.950          0.986    1.470  2.38e-01   35.60
12    14   0.8730 -1.870          0.986    0.802  8.27e-02   24.50
13    16   0.8820 -1.800          0.979    0.468  3.12e-02   17.30
14    18   0.9180 -1.690          0.985    0.288  1.19e-02   12.50
15    20   0.9420 -1.600          0.988    0.185  4.79e-03    9.16

Power	SFT.R.sq	slope	truncated.R.sq	mean.k.	median.k.	max.k.
1	0.08682157	0.8820601	0.8877917	1081.1068565	1.089741e+03	1686.156755
2	0.28622457	-1.1729565	0.8631891	336.3461812	3.222064e+02	798.575992
3	0.57483023	-1.7238558	0.9230250	133.0766539	1.155664e+02	460.255658
4	0.67059084	-2.0210959	0.9346949	61.4749048	4.700680e+01	296.282031
5	0.73662969	-2.1024598	0.9538173	31.6924296	2.089565e+01	204.558497
6	0.74338186	-2.2197752	0.9564366	17.7373675	9.852889e+00	148.173791
7	0.77934389	-2.1914854	0.9684850	10.5815646	4.915240e+00	111.129137
8	0.79898550	-2.1545864	0.9744351	6.6431563	2.525501e+00	85.561574
9	0.81862291	-2.1163663	0.9783691	4.3482460	1.346482e+00	67.234901
10	0.83443100	-2.0512651	0.9824172	2.9466684	7.411700e-01	53.700873
12	0.85590807	-1.9520372	0.9863926	1.4714913	2.384285e-01	35.566779
14	0.87303836	-1.8717587	0.9862762	0.8021158	8.270069e-02	24.454629
16	0.88236278	-1.7975866	0.9794021	0.4677393	3.116421e-02	17.284522
18	0.91753298	-1.6901870	0.9847788	0.2877587	1.192253e-02	12.479439
20	0.94216559	-1.6019139	0.9880597	0.1849243	4.786690e-03	9.164832

	Power	mean.k.
9	9	4.3482460
10	10	2.9466684
11	12	1.4714913
12	14	0.8021158
13	16	0.4677393
14	18	0.2877587
15	20	0.1849243

Parameters for network construction

• Soft-thresholding power parameter: 9 (R2 > 0.80 and mean connectivity highest as possible (Ref: https://www.degruyter.com/view/j/sagmb.2005.4.issue-1/sagmb.2005.4.1.1128/sagmb.2005.4.1.1128.pdf))
• Minimum module size: 30
• Height for module merging: 0.25 (below)
• Biweight Midcorrelation

 Calculating module eigengenes block-wise from all genes
   Flagging genes and samples with too many missing values...
    ..step 1
 ....pre-clustering genes to determine blocks..
   Projective K-means:
   ..k-means clustering..
   ..merging smaller clusters...
Block sizes:
gBlocks
   1    2 
7606 3564 
 ..Working on block 1 .
    TOM calculation: adjacency..
    ..will use 4 parallel threads.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
   ..saving TOM for block 1 into file norm_genes_TOM-block.1.RData
 ....clustering..
 ....detecting modules..
 ....calculating module eigengenes..
 ....checking kME in modules..
     ..removing 2 genes from module 1 because their KME is too low.
     ..removing 1 genes from module 6 because their KME is too low.
 ..Working on block 2 .
    TOM calculation: adjacency..
    ..will use 4 parallel threads.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
   ..saving TOM for block 2 into file norm_genes_TOM-block.2.RData
 ....clustering..
 ....detecting modules..
 ....calculating module eigengenes..
 ....checking kME in modules..
     ..removing 2 genes from module 2 because their KME is too low.
     ..removing 3 genes from module 4 because their KME is too low.
 ..merging modules that are too close..
     mergeCloseModules: Merging modules whose distance is less than 0.35
       Calculating new MEs...

 ME0  ME1  ME2  ME3  ME4  ME5  ME6  ME7  ME8  ME9 ME10 ME11 
6174 1565  806  781  612  374  324  179  162   80   73   40 

11

• 11 modules with between 40 and 1565 genes
• 6174 genes not assigned to a module

4996

4996

0

'grey'

1

'turquoise'

2

'blue'

3

'brown'

4

'yellow'

5

'green'

6

'red'

7

'black'

8

'pink'

9

'magenta'

10

'purple'

11

'greenyellow'

Network visualization

TOM calculation: adjacency..
..will use 4 parallel threads.
 Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.

	0610007P14Rik	0610009B22Rik	0610009O20Rik	0610010K14Rik	Mettl26	0610030E20Rik	0610037L13Rik	Fmc1	1110004F10Rik	Card19	⋯	Zswim6	Zswim7	Zswim8	Zufsp	Zxda	Zyg11b	Zyx	Zzef1	Zzz3	Hikeshi
0610007P14Rik	1	1	0	0	0	0	0	0	0	0	⋯	0	0	1	0	0	0	0	0	0	0
0610009B22Rik	1	1	0	0	0	0	0	0	0	0	⋯	0	0	0	0	0	0	0	0	0	1
0610009O20Rik	0	0	1	0	0	0	0	0	0	0	⋯	0	0	1	0	0	0	0	0	0	0
0610010K14Rik	0	0	0	1	0	0	0	1	0	1	⋯	0	1	0	0	0	1	0	0	0	1
Mettl26	0	0	0	0	1	0	0	0	0	1	⋯	0	0	0	0	0	0	0	0	0	0
0610030E20Rik	0	0	0	0	0	1	1	0	0	0	⋯	1	0	1	1	0	0	0	1	1	0

0610007P14Rik

'4'

0610009B22Rik

'5'

0610009O20Rik

'1'

0610010K14Rik

'4'

Mettl26

'4'

0610030E20Rik

'1'

4

'yellow'

5

'green'

1

'turquoise'

4

'yellow'

4

'yellow'

1

'turquoise'

Module analysis

1565

[1] 1

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
17799 GO:0090304            6.732271e-37                        1        566
5756  GO:0016070            1.348307e-32                        1        511
3020  GO:0006139            3.396777e-29                        1        581
12953 GO:0046483            6.883528e-28                        1        584
4834  GO:0010467            1.653568e-27                        1        556
3420  GO:0006725            1.060674e-26                        1        585
      numInCat                                             term ontology
17799     4325                   nucleic acid metabolic process       BP
5756      3872                            RNA metabolic process       BP
3020      4848 nucleobase-containing compound metabolic process       BP
12953     4947                    heterocycle metabolic process       BP
4834      4726                                  gene expression       BP
3420      5011     cellular aromatic compound metabolic process       BP
[1] 2

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
16368 GO:0070647            3.091339e-13                        1         80
5997  GO:0016567            1.909439e-12                        1         67
14460 GO:0051603            2.417010e-12                        1         67
8648  GO:0032446            4.636519e-12                        1         69
11979 GO:0044257            2.173275e-11                        1         67
7417  GO:0030163            2.493776e-11                        1         75
      numInCat                                                         term
16368      694 protein modification by small protein conjugation or removal
5997       541                                       protein ubiquitination
14460      590   proteolysis involved in cellular protein catabolic process
8648       582            protein modification by small protein conjugation
11979      622                           cellular protein catabolic process
7417       745                                    protein catabolic process
      ontology
16368       BP
5997        BP
14460       BP
8648        BP
11979       BP
7417        BP
[1] 3

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
16937 GO:0071704            2.743919e-23                        1        490
11965 GO:0044238            4.928763e-23                        1        470
3974  GO:0008152            3.120018e-22                        1        502
11964 GO:0044237            5.312527e-22                        1        466
4377  GO:0009056            2.322063e-20                        1        139
12158 GO:0044710            5.886847e-20                        1        232
      numInCat                                term ontology
16937     9446 organic substance metabolic process       BP
11965     8887           primary metabolic process       BP
3974      9868                   metabolic process       BP
11964     8866          cellular metabolic process       BP
4377      1611                   catabolic process       BP
12158     3454   single-organism metabolic process       BP
[1] 4

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
9705  GO:0034641            4.807047e-33                        1        250
11964 GO:0044237            1.535082e-32                        1        339
3974  GO:0008152            4.655645e-32                        1        370
17005 GO:0071840            1.196809e-30                        1        233
3590  GO:0007005            2.174423e-30                        1         78
3465  GO:0006807            7.690920e-30                        1        252
      numInCat                                          term ontology
9705      5508  cellular nitrogen compound metabolic process       BP
11964     8866                    cellular metabolic process       BP
3974      9868                             metabolic process       BP
17005     5620 cellular component organization or biogenesis       BP
3590       621                    mitochondrion organization       BP
3465      5831           nitrogen compound metabolic process       BP
[1] 5

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
11972 GO:0044248            1.349996e-10                        1         58
12359 GO:0045184            3.791994e-09                        1         68
11984 GO:0044265            4.130686e-09                        1         40
4378  GO:0009057            7.501194e-09                        1         45
4377  GO:0009056            1.754315e-08                        1         61
18903 GO:1901575            2.194517e-08                        1         59
      numInCat                                     term ontology
11972     1304               cellular catabolic process       BP
12359     1809    establishment of protein localization       BP
11984      793 cellular macromolecule catabolic process       BP
4378       980          macromolecule catabolic process       BP
4377      1611                        catabolic process       BP
18903     1540      organic substance catabolic process       BP
[1] 6

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
3557  GO:0006952            7.626613e-19                        1         66
3560  GO:0006955            2.189496e-18                        1         60
1052  GO:0002376            1.020968e-17                        1         87
10116 GO:0035456            1.376979e-16                        1         15
4620  GO:0009605            5.104588e-15                        1         76
3556  GO:0006950            1.960846e-14                        1        103
      numInCat                          term ontology
3557      1323              defense response       BP
3560      1110               immune response       BP
1052      2158         immune system process       BP
10116       46   response to interferon-beta       BP
4620      1907 response to external stimulus       BP
3556      3099            response to stress       BP
[1] 7

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
12158 GO:0044710            1.973405e-07                0.9999999         58
13556 GO:0048518            2.788819e-07                0.9999999         74
13560 GO:0048522            1.398066e-06                0.9999994         67
11965 GO:0044238            1.443017e-06                0.9999993        108
5242  GO:0014067            2.674909e-06                1.0000000          4
16937 GO:0071704            3.986056e-06                0.9999981        111
      numInCat                                                           term
12158     3454                              single-organism metabolic process
13556     4974                      positive regulation of biological process
13560     4482                        positive regulation of cellular process
11965     8887                                      primary metabolic process
5242        12 negative regulation of phosphatidylinositol 3-kinase signaling
16937     9446                            organic substance metabolic process
      ontology
12158       BP
13556       BP
13560       BP
11965       BP
5242        BP
16937       BP
[1] 8

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
3468  GO:0006810            2.240896e-05                0.9999895         57
14240 GO:0051234            3.402958e-05                0.9999837         58
3458  GO:0006790            4.123608e-05                0.9999931         10
      numInCat                              term ontology
3468      4082                         transport       BP
14240     4231     establishment of localization       BP
3458       262 sulfur compound metabolic process       BP
[1] 9

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

[1] category                 over_represented_pvalue  under_represented_pvalue
[4] numDEInCat               numInCat                 term                    
[7] ontology                
<0 rows> (or 0-length row.names)
[1] 10

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
15    GO:0000028                       0                        1          8
936   GO:0002181                       0                        1          9
3177  GO:0006412                       0                        1         41
3251  GO:0006518                       0                        1         41
10964 GO:0042255                       0                        1          9
10976 GO:0042274                       0                        1         12
      numInCat                               term ontology
15          19   ribosomal small subunit assembly       BP
936         49            cytoplasmic translation       BP
3177       597                        translation       BP
3251       738          peptide metabolic process       BP
10964       52                  ribosome assembly       BP
10976       66 ribosomal small subunit biogenesis       BP
[1] 11

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

[1] category                 over_represented_pvalue  under_represented_pvalue
[4] numDEInCat               numInCat                 term                    
[7] ontology                
<0 rows> (or 0-length row.names)

<!DOCTYPE html>

[1] "1: 40 - 2.55591054313099%"
[1] "2: 41 - 5.08684863523573%"
[1] "3: 17 - 2.17669654289373%"
[1] "4: 15 - 2.45098039215686%"
[1] "5: 14 - 3.74331550802139%"
[1] "6: 7 - 2.16049382716049%"
[1] "7: 3 - 1.67597765363128%"
[1] "8: 8 - 4.93827160493827%"
[1] "9: 2 - 2.5%"
[1] "10: 3 - 4.10958904109589%"
[1] "11: 0 - 0%"

Relation between modules and samples

Functional gene network

1. 6537
2. 24421

Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”

1. 1341
2. 182
3. 1513

Tree with all GOs at "../results/dge/global_GO_network.png"

1. FALSE
2. FALSE
3. FALSE

6537

6207

5643

$`0610009O20RIK`

1. 'GO:0006508'
2. 'GO:0006915'
3. 'GO:0007154'
4. 'GO:0007165'
5. 'GO:0007166'
6. 'GO:0008152'
7. 'GO:0008219'
8. 'GO:0009987'
9. 'GO:0010941'
10. 'GO:0012501'
11. 'GO:0019222'
12. 'GO:0019538'
13. 'GO:0023052'
14. 'GO:0042981'
15. 'GO:0043067'
16. 'GO:0043170'
17. 'GO:0043281'
18. 'GO:0044238'
19. 'GO:0044699'
20. 'GO:0044700'
21. 'GO:0044763'
22. 'GO:0050789'
23. 'GO:0050790'
24. 'GO:0050794'
25. 'GO:0050896'
26. 'GO:0051246'
27. 'GO:0051716'
28. 'GO:0060255'
29. 'GO:0065007'
30. 'GO:0071704'
31. 'GO:0080090'
32. 'GO:0097190'
33. 'GO:0005622'
34. 'GO:0005623'
35. 'GO:0005737'
36. 'GO:0043226'
37. 'GO:0043227'
38. 'GO:0043229'
39. 'GO:0043231'
40. 'GO:0044424'
41. 'GO:0044464'

$FMC1

1. 'GO:0008152'
2. 'GO:0008283'
3. 'GO:0009987'
4. 'GO:0019222'
5. 'GO:0042127'
6. 'GO:0044238'
7. 'GO:0044699'
8. 'GO:0048519'
9. 'GO:0050789'
10. 'GO:0050794'
11. 'GO:0061469'
12. 'GO:0065007'
13. 'GO:0071704'
14. 'GO:0080090'
15. 'GO:0005622'
16. 'GO:0005623'
17. 'GO:0005737'
18. 'GO:0043226'
19. 'GO:0043227'
20. 'GO:0043229'
21. 'GO:0043231'
22. 'GO:0044424'
23. 'GO:0044464'

$`1190002N15RIK`

1. 'GO:0007154'
2. 'GO:0007165'
3. 'GO:0007275'
4. 'GO:0008283'
5. 'GO:0009966'
6. 'GO:0009987'
7. 'GO:0010646'
8. 'GO:0023051'
9. 'GO:0023052'
10. 'GO:0032501'
11. 'GO:0032502'
12. 'GO:0035556'
13. 'GO:0044699'
14. 'GO:0044700'
15. 'GO:0044707'
16. 'GO:0044763'
17. 'GO:0044767'
18. 'GO:0048513'
19. 'GO:0048583'
20. 'GO:0048731'
21. 'GO:0048856'
22. 'GO:0050789'
23. 'GO:0050794'
24. 'GO:0050896'
25. 'GO:0051179'
26. 'GO:0051716'
27. 'GO:0065007'
28. 'GO:1902531'
29. 'GO:0005576'
30. 'GO:0005615'
31. 'GO:0005622'
32. 'GO:0005623'
33. 'GO:0005737'
34. 'GO:0016020'
35. 'GO:0031982'
36. 'GO:0031988'
37. 'GO:0032991'
38. 'GO:0043226'
39. 'GO:0043227'
40. 'GO:0043229'
41. 'GO:0043231'
42. 'GO:0044421'
43. 'GO:0044422'
44. 'GO:0044424'
45. 'GO:0044425'
46. 'GO:0044446'
47. 'GO:0044464'

$`1600002K03RIK`

1. 'GO:0005576'
2. 'GO:0005622'
3. 'GO:0005623'
4. 'GO:0005737'
5. 'GO:0016020'
6. 'GO:0031224'
7. 'GO:0044424'
8. 'GO:0044425'
9. 'GO:0044464'

$`1600014C10RIK`

1. 'GO:0005622'
2. 'GO:0005623'
3. 'GO:0005737'
4. 'GO:0016020'
5. 'GO:0031224'
6. 'GO:0043226'
7. 'GO:0043227'
8. 'GO:0043229'
9. 'GO:0043231'
10. 'GO:0044424'
11. 'GO:0044425'
12. 'GO:0044464'

$`1700029J07RIK`

1. 'GO:0005622'
2. 'GO:0005623'
3. 'GO:0005737'
4. 'GO:0005856'
5. 'GO:0015630'
6. 'GO:0043226'
7. 'GO:0043228'
8. 'GO:0043229'
9. 'GO:0043232'
10. 'GO:0044422'
11. 'GO:0044424'
12. 'GO:0044430'
13. 'GO:0044446'
14. 'GO:0044464'

Median of gene counts in the modules over ages